Tim Site Directory Not Working & Thumb Script Needs to Be Removed (thump.php)

My site is not fully functioning. In the backend of my site it reads:

“ATTENTION: Insecure Version of Timthumb Image Resize Script Detected
A possible old version of the TimThumb script was detected in your theme folder. Please remove the following files from your theme as a security precaution:
– thumb.php ( found at /themes/canvas/thumb.php )”

In addition my permalinks I think have all changed, such that now all menu tabs are being redirected to a link in iTunes and search directory on site not working either. The site was completely broken earlier which GoDaddy fixed by:

“removing the base64 code from the index.php file and renamed it. but left an index file with the base64 code. should have an index.php.”

My site is https://www.vixely.com.

Please help! Thanks!